Protein target profile

KP13_31991

pyridoxamine 5'-phosphate oxidase

Genome: KpKP13 Gene: pdxH AHE44282.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GQR1
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Length 220
Pocket druggability 0.553
Direct ligand evidence 0 2 total records
Functional annotation 1 EC 4 GO
Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Main supporting evidence

Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Moderate predicted binding pocket FPocket selected-pocket score 0.55. This supports review but is not experimental validation. Structure available AlphaFold DB model + ColabFold model Ligand evidence via structure/bioactivity 2 structural and 0 bioactivity records.

Risks to review

Human similarity Top human hit identity: 47.403%. This target also has a predicted binding pocket (FPocket 0.55) — check the ligand evidence before deprioritizing on off-target risk alone. Microbiome similarity 164 of 4744 screened genomes (3.5%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 0.55) — check the ligand evidence before deprioritizing on off-target risk alone. Weak second pocket-predictor signal P2Rank predicted binding-site probability 0.14.

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for this protein.
Terms and data sources used on this page

PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.

AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.

ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.

pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.

FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.

Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.

PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.

ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.

ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.

LigQ / LigQ_2: an internal Target pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.

Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.

DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.

Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.

EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.

KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.

Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.

Prioritization evidence

Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.

Off-target risk

Human off-target
Hit
Human identity (%)
47.403 Lower values reduce human off-target concern.
Human E-value
2.3e-42
Gut microbiome similarity
3.5% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
93.119 Higher values support similarity to known essential genes.
DEG E-value
3.36e-154 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
94.79 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.553
Structure A0A0H3GQR1
Pocket Pocket 2
P2Rank 0.143
Structure A0A0H3GQR1
Pocket Pocket 1
ColabFold model
FPocket 0.972 · Pocket 1
P2Rank 0.182 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 164 / 4744 genomes with a hit
Prevalence 3.5%

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.

Sequence

UniProt A0A0H3GQR1

Sequence

Primary amino-acid sequence viewer.

MAMSDNDELQQIAHLRREYTRGGLRRHDLPAEPLPLFERWLRQACDAKLADPTAMVVATVDERGQPYQRIVLLKHYDEKGLVFYTNLGSRKAHQIENNPQVSLLFPWHMLERQVMVIGKAERLSTLEVVKYFHSRPRDSQIGAWVSKQSSRISARGILESKFLELKQKFQQGEVPLPSFWGGFRVSIEQMEFWQGGEHRLHDRFLYQRDSGAWKIDRLAP

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • GO:0016638 Catalysis of an oxidation-reduction (redox) reaction in which a CH-NH2 group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
  • GO:0008615 The chemical reactions and pathways resulting in the formation of pyridoxine, 2-methyl-3-hydroxy-4,5-bis(hydroxymethyl)pyridine, one of the vitamin B6 compounds.
  • GO:0004733 Catalysis of the reaction: pyridoxamine 5'-phosphate + H2O + O2 = pyridoxal 5'-phosphate + NH4+ + H2O2. This activity can also oxidize pyridoxine 5'-phosphate to pyridoxal 5'-phosphate + H2O2.
  • GO:0010181 Binding to flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

18 records
Show feature table
Start End DB Term Name
12 220 PANTHER PTHR10851 PYRIDOXINE-5-PHOSPHATE OXIDASE
12 220 InterPro IPR000659 Pyridoxamine 5'-phosphate oxidase
2 220 PIRSF PIRSF000190 Pyd_amn-ph_oxd
2 220 InterPro IPR000659 Pyridoxamine 5'-phosphate oxidase
22 220 Gene3D G3DSA:2.30.110.10 -
22 220 InterPro IPR012349 FMN-binding split barrel
43 124 Pfam PF01243 Pyridoxamine 5'-phosphate oxidase
43 124 InterPro IPR011576 Pyridoxamine 5'-phosphate oxidase, putative
22 220 FunFam G3DSA:2.30.110.10:FF:000001 Pyridoxine/pyridoxamine 5'-phosphate oxidase
180 220 Pfam PF10590 Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region
180 220 InterPro IPR019576 Pyridoxine 5'-phosphate oxidase, dimerisation, C-terminal
190 203 ProSitePatterns PS01064 Pyridoxamine 5'-phosphate oxidase signature.
190 203 InterPro IPR019740 Pyridoxamine 5'-phosphate oxidase, conserved site
23 220 SUPERFAMILY SSF50475 FMN-binding split barrel
18 220 Hamap MF_01629 Pyridoxine/pyridoxamine 5'-phosphate oxidase [pdxH].
18 220 InterPro IPR000659 Pyridoxamine 5'-phosphate oxidase
32 220 NCBIfam TIGR00558 pyridoxamine 5'-phosphate oxidase
32 220 InterPro IPR000659 Pyridoxamine 5'-phosphate oxidase

3D structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.

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Pocket score High Medium Low
How colors and pocket overlays are used
Uniform protein color marks the displayed model as a single molecular object.
Experimental PDB structures may be colored by chain to distinguish subunits or copies present in the file.
Pocket colors and alpha spheres are evidence overlays for predicted binding cavities; they are not alternative protein chains.
'Alpha spheres' is FPocket's own cavity-shape geometry, imported when available and aligned with the loaded structure.
'Pocket atoms'/'Predicted site atoms' show the pocket's residue atoms instead: P2Rank reports residues rather than alpha spheres, and FPocket falls back to this when alpha-sphere geometry is unavailable or doesn't align.
'No pocket geometry' means neither alpha spheres nor residue-position data could be found for that pocket; the layer just highlights the same residues as 'Nearby residues'.
Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · FPocket

Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Site 1 FPocket #2
0.553
Unusual size
Show in viewer
Surrounding area
Site 2 FPocket #5
0.539
Show in viewer
Surrounding area
Site 3 FPocket #9
0.204
Show in viewer
Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.143
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.004
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:113-113
UniProt: Binding site:131-131
UniProt: Binding site:135-135
UniProt: Binding site:139-139
UniProt: Binding site:148-149
UniProt: Binding site:16-19
UniProt: Binding site:193-193
UniProt: Binding site:199-201
UniProt: Binding site:203-203
UniProt: Binding site:69-74
UniProt: Binding site:74-74
UniProt: Binding site:84-85
UniProt: Binding site:90-90
UniProt: Binding site:91-91
All structural evidence 0 experimental · 2 predicted

Structural evidence

0 + 2

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold DB AF_A0A0H3GQR1
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_31991
ColabFold — — full sequence — Loaded

Ligand evidence

Ligands grouped by evidence source. PDB ligands keep the source crystal visible, and loaded crystals can be opened directly in the structure viewer.

2 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 2 records from similar proteins
Structural ligands 2 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 0 similarity-based ZINC candidates
Best available ligand signal
NNV PDB via homolog 274.3 Da · LogP 0.93 · TPSA 99.0 Open detail RCSB PDB
WUB PDB via homolog Detail RCSB PDB

Structural evidence inferred from similar proteins. The source crystal indicates where the ligand was observed; the UniProt column identifies the homologous protein carrying that ligand.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
NNV RCSB PDB
4HMT
Q51793 274.3 Da LogP 0.93 TPSA 99.0 ✓ Ro5 ✓ Clean C1C=CC2=NC3=C(C=CC[C@H]3C(=O)O)NC2[C@@H]1C(=O)O
WUB RCSB PDB
4HMX
Q396C5 228.3 Da LogP 2.21 TPSA 61.7 ✓ Ro5 ✓ Clean c1ccc2c(c1)N[C@H]3[C@@H](CC=CC3=N2)C(=O)O

PDB and ChEMBL records on this protein are shown in full. ChEMBL records from similar proteins are capped at the top 100 per protein (by pchembl) and ZINC at the top 50 (Tanimoto ≥ 0.5). ADME columns are descriptor-based screening flags, not experimental toxicity results.